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values | func_name stringlengths 1 134 | docstring stringlengths 1 46.9k | path stringlengths 4 223 | original_string stringlengths 75 104k | code stringlengths 75 104k | docstring_tokens listlengths 1 1.97k | repo stringlengths 7 55 | language stringclasses 1
value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
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train | XcFunc.from_abinit_ixc | Build the object from Abinit ixc (integer) | pymatgen/core/xcfunc.py | def from_abinit_ixc(cls, ixc):
"""Build the object from Abinit ixc (integer)"""
ixc = int(ixc)
if ixc >= 0:
return cls(**cls.abinitixc_to_libxc[ixc])
else:
# libxc notation employed in Abinit: a six-digit number in the form XXXCCC or CCCXXX
#ixc = str(... | def from_abinit_ixc(cls, ixc):
"""Build the object from Abinit ixc (integer)"""
ixc = int(ixc)
if ixc >= 0:
return cls(**cls.abinitixc_to_libxc[ixc])
else:
# libxc notation employed in Abinit: a six-digit number in the form XXXCCC or CCCXXX
#ixc = str(... | [
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train | XcFunc.from_type_name | Build the object from (type, name). | pymatgen/core/xcfunc.py | def from_type_name(cls, typ, name):
"""Build the object from (type, name)."""
# Try aliases first.
for k, nt in cls.defined_aliases.items():
if typ is not None and typ != nt.type: continue
#print(name, nt.name)
if name == nt.name:
if len(k) == ... | def from_type_name(cls, typ, name):
"""Build the object from (type, name)."""
# Try aliases first.
for k, nt in cls.defined_aliases.items():
if typ is not None and typ != nt.type: continue
#print(name, nt.name)
if name == nt.name:
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train | XcFunc.from_dict | Makes XcFunc obey the general json interface used in pymatgen for easier serialization. | pymatgen/core/xcfunc.py | def from_dict(cls, d):
"""
Makes XcFunc obey the general json interface used in pymatgen for easier serialization.
"""
return cls(xc=d.get("xc"), x=d.get("x"), c=d.get("c")) | def from_dict(cls, d):
"""
Makes XcFunc obey the general json interface used in pymatgen for easier serialization.
"""
return cls(xc=d.get("xc"), x=d.get("x"), c=d.get("c")) | [
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train | XcFunc.as_dict | Makes XcFunc obey the general json interface used in pymatgen for easier serialization. | pymatgen/core/xcfunc.py | def as_dict(self):
"""
Makes XcFunc obey the general json interface used in pymatgen for easier serialization.
"""
d = {"@module": self.__class__.__module__,
"@class": self.__class__.__name__}
# print("in as_dict", type(self.x), type(self.c), type(self.xc))
i... | def as_dict(self):
"""
Makes XcFunc obey the general json interface used in pymatgen for easier serialization.
"""
d = {"@module": self.__class__.__module__,
"@class": self.__class__.__name__}
# print("in as_dict", type(self.x), type(self.c), type(self.xc))
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"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
train | XcFunc.type | The type of the functional. | pymatgen/core/xcfunc.py | def type(self):
"""The type of the functional."""
if self.xc in self.defined_aliases: return self.defined_aliases[self.xc].type
xc = (self.x, self.c)
if xc in self.defined_aliases: return self.defined_aliases[xc].type
# If self is not in defined_aliases, use LibxcFunc family
... | def type(self):
"""The type of the functional."""
if self.xc in self.defined_aliases: return self.defined_aliases[self.xc].type
xc = (self.x, self.c)
if xc in self.defined_aliases: return self.defined_aliases[xc].type
# If self is not in defined_aliases, use LibxcFunc family
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train | XcFunc.name | The name of the functional. If the functional is not found in the aliases,
the string has the form X_NAME+C_NAME | pymatgen/core/xcfunc.py | def name(self):
"""
The name of the functional. If the functional is not found in the aliases,
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"""
if self.xc in self.defined_aliases: return self.defined_aliases[self.xc].name
xc = (self.x, self.c)
if xc in self.defined_alias... | def name(self):
"""
The name of the functional. If the functional is not found in the aliases,
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"""
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train | from_bson_voronoi_list | Returns the voronoi_list needed for the VoronoiContainer object from a bson-encoded voronoi_list (composed of
vlist and bson_nb_voro_list).
:param vlist: List of voronoi objects
:param bson_nb_voro_list: List of periodic sites involved in the Voronoi
:return: The voronoi_list needed for the VoronoiConta... | pymatgen/analysis/chemenv/coordination_environments/voronoi.py | def from_bson_voronoi_list(bson_nb_voro_list, structure):
"""
Returns the voronoi_list needed for the VoronoiContainer object from a bson-encoded voronoi_list (composed of
vlist and bson_nb_voro_list).
:param vlist: List of voronoi objects
:param bson_nb_voro_list: List of periodic sites involved in... | def from_bson_voronoi_list(bson_nb_voro_list, structure):
"""
Returns the voronoi_list needed for the VoronoiContainer object from a bson-encoded voronoi_list (composed of
vlist and bson_nb_voro_list).
:param vlist: List of voronoi objects
:param bson_nb_voro_list: List of periodic sites involved in... | [
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train | DetailedVoronoiContainer.setup_voronoi_list | Set up of the voronoi list of neighbours by calling qhull
:param indices: indices of the sites for which the Voronoi is needed
:param voronoi_cutoff: Voronoi cutoff for the search of neighbours
:raise RuntimeError: If an infinite vertex is found in the voronoi construction | pymatgen/analysis/chemenv/coordination_environments/voronoi.py | def setup_voronoi_list(self, indices, voronoi_cutoff):
"""
Set up of the voronoi list of neighbours by calling qhull
:param indices: indices of the sites for which the Voronoi is needed
:param voronoi_cutoff: Voronoi cutoff for the search of neighbours
:raise RuntimeError: If an ... | def setup_voronoi_list(self, indices, voronoi_cutoff):
"""
Set up of the voronoi list of neighbours by calling qhull
:param indices: indices of the sites for which the Voronoi is needed
:param voronoi_cutoff: Voronoi cutoff for the search of neighbours
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train | DetailedVoronoiContainer.setup_neighbors_distances_and_angles | Initializes the angle and distance separations
:param indices: indices of the sites for which the Voronoi is needed | pymatgen/analysis/chemenv/coordination_environments/voronoi.py | def setup_neighbors_distances_and_angles(self, indices):
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Initializes the angle and distance separations
:param indices: indices of the sites for which the Voronoi is needed
"""
self.neighbors_distances = [None] * len(self.structure)
self.neighbors_normalized_distances... | def setup_neighbors_distances_and_angles(self, indices):
"""
Initializes the angle and distance separations
:param indices: indices of the sites for which the Voronoi is needed
"""
self.neighbors_distances = [None] * len(self.structure)
self.neighbors_normalized_distances... | [
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train | DetailedVoronoiContainer.to_bson_voronoi_list2 | Transforms the voronoi_list into a vlist + bson_nb_voro_list, that are BSON-encodable.
:return: [vlist, bson_nb_voro_list], to be used in the as_dict method | pymatgen/analysis/chemenv/coordination_environments/voronoi.py | def to_bson_voronoi_list2(self):
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"""
bson_nb_voro_list2 = [None] * len(self.voronoi_list2)
for ivoro, voro in e... | def to_bson_voronoi_list2(self):
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Transforms the voronoi_list into a vlist + bson_nb_voro_list, that are BSON-encodable.
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bson_nb_voro_list2 = [None] * len(self.voronoi_list2)
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train | DetailedVoronoiContainer.as_dict | Bson-serializable dict representation of the VoronoiContainer.
:return: dictionary that is BSON-encodable | pymatgen/analysis/chemenv/coordination_environments/voronoi.py | def as_dict(self):
"""
Bson-serializable dict representation of the VoronoiContainer.
:return: dictionary that is BSON-encodable
"""
bson_nb_voro_list2 = self.to_bson_voronoi_list2()
return {"@module": self.__class__.__module__,
"@class": self.__class__.__... | def as_dict(self):
"""
Bson-serializable dict representation of the VoronoiContainer.
:return: dictionary that is BSON-encodable
"""
bson_nb_voro_list2 = self.to_bson_voronoi_list2()
return {"@module": self.__class__.__module__,
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train | DetailedVoronoiContainer.from_dict | Reconstructs the VoronoiContainer object from a dict representation of the VoronoiContainer created using
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:param d: dict representation of the VoronoiContainer object
:return: VoronoiContainer object | pymatgen/analysis/chemenv/coordination_environments/voronoi.py | def from_dict(cls, d):
"""
Reconstructs the VoronoiContainer object from a dict representation of the VoronoiContainer created using
the as_dict method.
:param d: dict representation of the VoronoiContainer object
:return: VoronoiContainer object
"""
structure = S... | def from_dict(cls, d):
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Reconstructs the VoronoiContainer object from a dict representation of the VoronoiContainer created using
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:return: VoronoiContainer object
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structure = S... | [
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train | check_spectator | Decorator for :class:`Node` methods. Raise `SpectatorNodeError`. | pymatgen/io/abinit/nodes.py | def check_spectator(node_method):
"""
Decorator for :class:`Node` methods. Raise `SpectatorNodeError`.
"""
from functools import wraps
@wraps(node_method)
def wrapper(*args, **kwargs):
node = args[0]
if node.in_spectator_mode:
#raise node.SpectatorError("You should no... | def check_spectator(node_method):
"""
Decorator for :class:`Node` methods. Raise `SpectatorNodeError`.
"""
from functools import wraps
@wraps(node_method)
def wrapper(*args, **kwargs):
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if node.in_spectator_mode:
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train | Status.from_string | Return a `Status` instance from its string representation. | pymatgen/io/abinit/nodes.py | def from_string(cls, s):
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train | Dependency.products | List of output files produces by self. | pymatgen/io/abinit/nodes.py | def products(self):
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train | Dependency.get_filepaths_and_exts | Returns the paths of the output files produced by self and its extensions | pymatgen/io/abinit/nodes.py | def get_filepaths_and_exts(self):
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filepaths = [prod.filepath for prod in self.products]
exts = [prod.ext for prod in self.products]
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train | Product.from_file | Build a :class:`Product` instance from a filepath. | pymatgen/io/abinit/nodes.py | def from_file(cls, filepath):
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train | NodeResults.from_node | Initialize an instance of `NodeResults` from a `Node` subclass. | pymatgen/io/abinit/nodes.py | def from_node(cls, node):
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train | Node.color_hex | Node color as Hex Triplet https://en.wikipedia.org/wiki/Web_colors#Hex_triplet | pymatgen/io/abinit/nodes.py | def color_hex(self):
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train | Node.name | The name of the node
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The name of the node
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train | Node.relworkdir | Return a relative version of the workdir | pymatgen/io/abinit/nodes.py | def relworkdir(self):
"""Return a relative version of the workdir"""
if getattr(self, "workdir", None) is None:
return None
try:
return os.path.relpath(self.workdir)
except OSError:
# current working directory may not be defined!
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train | Node.log_correction | This method should be called once we have fixed the problem associated to this event.
It adds a new entry in the correction history of the node.
Args:
event: :class:`AbinitEvent` that triggered the correction.
action (str): Human-readable string with info on the action perfomed ... | pymatgen/io/abinit/nodes.py | def log_correction(self, event, action):
"""
This method should be called once we have fixed the problem associated to this event.
It adds a new entry in the correction history of the node.
Args:
event: :class:`AbinitEvent` that triggered the correction.
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"""
This method should be called once we have fixed the problem associated to this event.
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event: :class:`AbinitEvent` that triggered the correction.
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train | Node.add_deps | Add a list of dependencies to the :class:`Node`.
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"""
Add a list of dependencies to the :class:`Node`.
Args:
deps: List of :class:`Dependency` objects specifying the dependencies of the node.
or dictionary mapping nodes to file extensions e.g. {task: "DEN"}
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Add a list of dependencies to the :class:`Node`.
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deps: List of :class:`Dependency` objects specifying the dependencies of the node.
or dictionary mapping nodes to file extensions e.g. {task: "DEN"}
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train | Node.remove_deps | Remove a list of dependencies from the :class:`Node`.
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"""
Remove a list of dependencies from the :class:`Node`.
Args:
deps: List of :class:`Dependency` objects specifying the dependencies of the node.
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Remove a list of dependencies from the :class:`Node`.
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deps: List of :class:`Dependency` objects specifying the dependencies of the node.
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train | Node.deps_status | Returns a list with the status of the dependencies. | pymatgen/io/abinit/nodes.py | def deps_status(self):
"""Returns a list with the status of the dependencies."""
if not self.deps:
return [self.S_OK]
return [d.status for d in self.deps] | def deps_status(self):
"""Returns a list with the status of the dependencies."""
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train | Node.get_children | Return the list of nodes in the :class:`Flow` that depends on this :class:`Node`
.. note::
This routine assumes the entire flow has been allocated. | pymatgen/io/abinit/nodes.py | def get_children(self):
"""
Return the list of nodes in the :class:`Flow` that depends on this :class:`Node`
.. note::
This routine assumes the entire flow has been allocated.
"""
# Specialized branch for FileNode.
if self.is_file:
return self.fi... | def get_children(self):
"""
Return the list of nodes in the :class:`Flow` that depends on this :class:`Node`
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train | Node.str_deps | Return the string representation of the dependencies of the node. | pymatgen/io/abinit/nodes.py | def str_deps(self):
"""Return the string representation of the dependencies of the node."""
lines = []
app = lines.append
app("Dependencies of node %s:" % str(self))
for i, dep in enumerate(self.deps):
app("%d) %s, status=%s" % (i, dep.info, str(dep.status)))
... | def str_deps(self):
"""Return the string representation of the dependencies of the node."""
lines = []
app = lines.append
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for i, dep in enumerate(self.deps):
app("%d) %s, status=%s" % (i, dep.info, str(dep.status)))
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train | Node.get_vars_dataframe | Return pandas DataFrame with the value of the variables specified in `varnames`.
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.. example:
flow.get_vars_dataframe("ecut", "ngkpt")
work.get_vars_dataframe("acell", "usepawu") | pymatgen/io/abinit/nodes.py | def get_vars_dataframe(self, *varnames):
"""
Return pandas DataFrame with the value of the variables specified in `varnames`.
Can be used for task/works/flow. It's recursive!
.. example:
flow.get_vars_dataframe("ecut", "ngkpt")
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Return pandas DataFrame with the value of the variables specified in `varnames`.
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train | Node.get_graphviz_dirtree | Generate directory graph in the DOT language. The graph show the files and directories
in the node workdir.
Returns: graphviz.Digraph <https://graphviz.readthedocs.io/en/stable/api.html#digraph> | pymatgen/io/abinit/nodes.py | def get_graphviz_dirtree(self, engine="automatic", **kwargs):
"""
Generate directory graph in the DOT language. The graph show the files and directories
in the node workdir.
Returns: graphviz.Digraph <https://graphviz.readthedocs.io/en/stable/api.html#digraph>
"""
if eng... | def get_graphviz_dirtree(self, engine="automatic", **kwargs):
"""
Generate directory graph in the DOT language. The graph show the files and directories
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Returns: graphviz.Digraph <https://graphviz.readthedocs.io/en/stable/api.html#digraph>
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train | Node.event_handlers | The list of handlers registered for this node.
If the node is not a `Flow` and does not have its own list of
`handlers` the handlers registered at the level of the flow are returned.
This trick allows one to registered different handlers at the level of the Task
for testing purposes. By... | pymatgen/io/abinit/nodes.py | def event_handlers(self):
"""
The list of handlers registered for this node.
If the node is not a `Flow` and does not have its own list of
`handlers` the handlers registered at the level of the flow are returned.
This trick allows one to registered different handlers at the leve... | def event_handlers(self):
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The list of handlers registered for this node.
If the node is not a `Flow` and does not have its own list of
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train | Node.install_event_handlers | Install the `EventHandlers for this `Node`. If no argument is provided
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Args:
categories: List of categories to install e.g. base + can_change_physics
handlers: explicit list of :class:`EventHandler` instances.
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"""
Install the `EventHandlers for this `Node`. If no argument is provided
the default list of handlers is installed.
Args:
categories: List of categories to install e.g. base + can_change_physics
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"""
Install the `EventHandlers for this `Node`. If no argument is provided
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categories: List of categories to install e.g. base + can_change_physics
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train | Node.show_event_handlers | Print to `stream` the event handlers installed for this flow. | pymatgen/io/abinit/nodes.py | def show_event_handlers(self, stream=sys.stdout, verbose=0):
"""Print to `stream` the event handlers installed for this flow."""
lines = ["List of event handlers installed:"]
for handler in self.event_handlers:
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train | Node.send_signal | Send signal from this node to all connected receivers unless the node is in spectator mode.
signal -- (hashable) signal value, see `dispatcher` connect for details
Return a list of tuple pairs [(receiver, response), ... ]
or None if the node is in spectator mode.
if any receiver raise... | pymatgen/io/abinit/nodes.py | def send_signal(self, signal):
"""
Send signal from this node to all connected receivers unless the node is in spectator mode.
signal -- (hashable) signal value, see `dispatcher` connect for details
Return a list of tuple pairs [(receiver, response), ... ]
or None if the node i... | def send_signal(self, signal):
"""
Send signal from this node to all connected receivers unless the node is in spectator mode.
signal -- (hashable) signal value, see `dispatcher` connect for details
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train | HistoryRecord.get_message | Return the message after merging any user-supplied arguments with the message.
Args:
metadata: True if function and module name should be added.
asctime: True if time string should be added. | pymatgen/io/abinit/nodes.py | def get_message(self, metadata=False, asctime=True):
"""
Return the message after merging any user-supplied arguments with the message.
Args:
metadata: True if function and module name should be added.
asctime: True if time string should be added.
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"""
Return the message after merging any user-supplied arguments with the message.
Args:
metadata: True if function and module name should be added.
asctime: True if time string should be added.
"""
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train | NodeHistory.to_string | Returns a string with the history. Set metadata to True to have info on function and module. | pymatgen/io/abinit/nodes.py | def to_string(self, metadata=False):
"""Returns a string with the history. Set metadata to True to have info on function and module."""
return "\n".join(rec.get_message(metadata=metadata) for rec in self) | def to_string(self, metadata=False):
"""Returns a string with the history. Set metadata to True to have info on function and module."""
return "\n".join(rec.get_message(metadata=metadata) for rec in self) | [
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train | NodeHistory.warning | Log 'msg % args' with the warning severity level | pymatgen/io/abinit/nodes.py | def warning(self, msg, *args, **kwargs):
"""Log 'msg % args' with the warning severity level"""
self._log("WARNING", msg, args, kwargs) | def warning(self, msg, *args, **kwargs):
"""Log 'msg % args' with the warning severity level"""
self._log("WARNING", msg, args, kwargs) | [
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train | NodeHistory.critical | Log 'msg % args' with the critical severity level | pymatgen/io/abinit/nodes.py | def critical(self, msg, *args, **kwargs):
"""Log 'msg % args' with the critical severity level"""
self._log("CRITICAL", msg, args, kwargs) | def critical(self, msg, *args, **kwargs):
"""Log 'msg % args' with the critical severity level"""
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train | NodeHistory._log | Low-level logging routine which creates a :class:`HistoryRecord`. | pymatgen/io/abinit/nodes.py | def _log(self, level, msg, args, exc_info=None, extra=None):
"""Low-level logging routine which creates a :class:`HistoryRecord`."""
if exc_info and not isinstance(exc_info, tuple):
exc_info = sys.exc_info()
self.append(HistoryRecord(level, "unknown filename", 0, msg, args, exc_info... | def _log(self, level, msg, args, exc_info=None, extra=None):
"""Low-level logging routine which creates a :class:`HistoryRecord`."""
if exc_info and not isinstance(exc_info, tuple):
exc_info = sys.exc_info()
self.append(HistoryRecord(level, "unknown filename", 0, msg, args, exc_info... | [
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train | parse_libxc_docs | Parse libxc_docs.txt file, return dictionary with mapping:
libxc_id --> info_dict | dev_scripts/regen_libxcfunc.py | def parse_libxc_docs(path):
"""
Parse libxc_docs.txt file, return dictionary with mapping:
libxc_id --> info_dict
"""
def parse_section(section):
d = {}
for l in section:
key, value = l.split(":")
key = key.strip()
d[key] = value.strip()
return int(d["Number"]), d
d = Ordered... | def parse_libxc_docs(path):
"""
Parse libxc_docs.txt file, return dictionary with mapping:
libxc_id --> info_dict
"""
def parse_section(section):
d = {}
for l in section:
key, value = l.split(":")
key = key.strip()
d[key] = value.strip()
return int(d["Number"]), d
d = Ordered... | [
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train | write_libxc_docs_json | Write json file with libxc metadata to path jpath. | dev_scripts/regen_libxcfunc.py | def write_libxc_docs_json(xcfuncs, jpath):
"""Write json file with libxc metadata to path jpath."""
from copy import deepcopy
xcfuncs = deepcopy(xcfuncs)
# Remove XC_FAMILY from Family and XC_ from Kind to make strings more human-readable.
for d in xcfuncs.values():
d["Family"] = d["Family"... | def write_libxc_docs_json(xcfuncs, jpath):
"""Write json file with libxc metadata to path jpath."""
from copy import deepcopy
xcfuncs = deepcopy(xcfuncs)
# Remove XC_FAMILY from Family and XC_ from Kind to make strings more human-readable.
for d in xcfuncs.values():
d["Family"] = d["Family"... | [
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train | main | Main function. | dev_scripts/regen_libxcfunc.py | def main():
"""Main function."""
if "-h" in sys.argv or "--help" in sys.argv:
print(__doc__)
print("Usage: regen_libxcfunc.py path_to_libxc_docs.txt")
return 0
try:
path = sys.argv[1]
except IndexError:
print(__doc__)
print("Usage: regen_libxcfunc.py path... | def main():
"""Main function."""
if "-h" in sys.argv or "--help" in sys.argv:
print(__doc__)
print("Usage: regen_libxcfunc.py path_to_libxc_docs.txt")
return 0
try:
path = sys.argv[1]
except IndexError:
print(__doc__)
print("Usage: regen_libxcfunc.py path... | [
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train | make_movie | Generate a movie from a sequence of structures using vtk and ffmpeg.
Args:
structures ([Structure]): sequence of structures
output_filename (str): filename for structure output. defaults to
movie.mp4
zoom (float): A zoom to be applied to the visualizer. Defaults to 1.0.
... | pymatgen/vis/structure_vtk.py | def make_movie(structures, output_filename="movie.mp4", zoom=1.0, fps=20,
bitrate="10000k", quality=1, **kwargs):
"""
Generate a movie from a sequence of structures using vtk and ffmpeg.
Args:
structures ([Structure]): sequence of structures
output_filename (str): filename fo... | def make_movie(structures, output_filename="movie.mp4", zoom=1.0, fps=20,
bitrate="10000k", quality=1, **kwargs):
"""
Generate a movie from a sequence of structures using vtk and ffmpeg.
Args:
structures ([Structure]): sequence of structures
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train | StructureVis.rotate_view | Rotate the camera view.
Args:
axis_ind: Index of axis to rotate. Defaults to 0, i.e., a-axis.
angle: Angle to rotate by. Defaults to 0. | pymatgen/vis/structure_vtk.py | def rotate_view(self, axis_ind=0, angle=0):
"""
Rotate the camera view.
Args:
axis_ind: Index of axis to rotate. Defaults to 0, i.e., a-axis.
angle: Angle to rotate by. Defaults to 0.
"""
camera = self.ren.GetActiveCamera()
if axis_ind == 0:
... | def rotate_view(self, axis_ind=0, angle=0):
"""
Rotate the camera view.
Args:
axis_ind: Index of axis to rotate. Defaults to 0, i.e., a-axis.
angle: Angle to rotate by. Defaults to 0.
"""
camera = self.ren.GetActiveCamera()
if axis_ind == 0:
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train | StructureVis.write_image | Save render window to an image.
Arguments:
filename:
filename to save to. Defaults to image.png.
magnification:
magnification. Use it to render high res images.
image_format:
choose between jpeg, png. Png is the default. | pymatgen/vis/structure_vtk.py | def write_image(self, filename="image.png", magnification=1,
image_format="png"):
"""
Save render window to an image.
Arguments:
filename:
filename to save to. Defaults to image.png.
magnification:
magnification. Use it... | def write_image(self, filename="image.png", magnification=1,
image_format="png"):
"""
Save render window to an image.
Arguments:
filename:
filename to save to. Defaults to image.png.
magnification:
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train | StructureVis.redraw | Redraw the render window.
Args:
reset_camera: Set to True to reset the camera to a
pre-determined default for each structure. Defaults to False. | pymatgen/vis/structure_vtk.py | def redraw(self, reset_camera=False):
"""
Redraw the render window.
Args:
reset_camera: Set to True to reset the camera to a
pre-determined default for each structure. Defaults to False.
"""
self.ren.RemoveAllViewProps()
self.picker = None
... | def redraw(self, reset_camera=False):
"""
Redraw the render window.
Args:
reset_camera: Set to True to reset the camera to a
pre-determined default for each structure. Defaults to False.
"""
self.ren.RemoveAllViewProps()
self.picker = None
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train | StructureVis.display_help | Display the help for various keyboard shortcuts. | pymatgen/vis/structure_vtk.py | def display_help(self):
"""
Display the help for various keyboard shortcuts.
"""
helptxt = ["h : Toggle help",
"A/a, B/b or C/c : Increase/decrease cell by one a,"
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"-: Tog... | def display_help(self):
"""
Display the help for various keyboard shortcuts.
"""
helptxt = ["h : Toggle help",
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" b or c unit vector", "# : Toggle showing of polyhedrons",
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train | StructureVis.set_structure | Add a structure to the visualizer.
Args:
structure: structure to visualize
reset_camera: Set to True to reset the camera to a default
determined based on the structure.
to_unit_cell: Whether or not to fall back sites into the unit cell. | pymatgen/vis/structure_vtk.py | def set_structure(self, structure, reset_camera=True, to_unit_cell=True):
"""
Add a structure to the visualizer.
Args:
structure: structure to visualize
reset_camera: Set to True to reset the camera to a default
determined based on the structure.
... | def set_structure(self, structure, reset_camera=True, to_unit_cell=True):
"""
Add a structure to the visualizer.
Args:
structure: structure to visualize
reset_camera: Set to True to reset the camera to a default
determined based on the structure.
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train | StructureVis.zoom | Zoom the camera view by a factor. | pymatgen/vis/structure_vtk.py | def zoom(self, factor):
"""
Zoom the camera view by a factor.
"""
camera = self.ren.GetActiveCamera()
camera.Zoom(factor)
self.ren_win.Render() | def zoom(self, factor):
"""
Zoom the camera view by a factor.
"""
camera = self.ren.GetActiveCamera()
camera.Zoom(factor)
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train | StructureVis.show | Display the visualizer. | pymatgen/vis/structure_vtk.py | def show(self):
"""
Display the visualizer.
"""
self.iren.Initialize()
self.ren_win.SetSize(800, 800)
self.ren_win.SetWindowName(self.title)
self.ren_win.Render()
self.iren.Start() | def show(self):
"""
Display the visualizer.
"""
self.iren.Initialize()
self.ren_win.SetSize(800, 800)
self.ren_win.SetWindowName(self.title)
self.ren_win.Render()
self.iren.Start() | [
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train | StructureVis.add_site | Add a site to the render window. The site is displayed as a sphere, the
color of which is determined based on the element. Partially occupied
sites are displayed as a single element color, though the site info
still shows the partial occupancy.
Args:
site: Site to add. | pymatgen/vis/structure_vtk.py | def add_site(self, site):
"""
Add a site to the render window. The site is displayed as a sphere, the
color of which is determined based on the element. Partially occupied
sites are displayed as a single element color, though the site info
still shows the partial occupancy.
... | def add_site(self, site):
"""
Add a site to the render window. The site is displayed as a sphere, the
color of which is determined based on the element. Partially occupied
sites are displayed as a single element color, though the site info
still shows the partial occupancy.
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train | StructureVis.add_text | Add text at a coordinate.
Args:
coords: Coordinates to add text at.
text: Text to place.
color: Color for text as RGB. Defaults to black. | pymatgen/vis/structure_vtk.py | def add_text(self, coords, text, color=(0, 0, 0)):
"""
Add text at a coordinate.
Args:
coords: Coordinates to add text at.
text: Text to place.
color: Color for text as RGB. Defaults to black.
"""
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"""
Add text at a coordinate.
Args:
coords: Coordinates to add text at.
text: Text to place.
color: Color for text as RGB. Defaults to black.
"""
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train | StructureVis.add_line | Adds a line.
Args:
start: Starting coordinates for line.
end: Ending coordinates for line.
color: Color for text as RGB. Defaults to grey.
width: Width of line. Defaults to 1. | pymatgen/vis/structure_vtk.py | def add_line(self, start, end, color=(0.5, 0.5, 0.5), width=1):
"""
Adds a line.
Args:
start: Starting coordinates for line.
end: Ending coordinates for line.
color: Color for text as RGB. Defaults to grey.
width: Width of line. Defaults to 1.
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Adds a line.
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start: Starting coordinates for line.
end: Ending coordinates for line.
color: Color for text as RGB. Defaults to grey.
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train | StructureVis.add_polyhedron | Adds a polyhedron.
Args:
neighbors: Neighbors of the polyhedron (the vertices).
center: The atom in the center of the polyhedron.
color: Color for text as RGB.
opacity: Opacity of the polyhedron
draw_edges: If set to True, the a line will be drawn at ... | pymatgen/vis/structure_vtk.py | def add_polyhedron(self, neighbors, center, color, opacity=1.0,
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"""
Adds a polyhedron.
Args:
neighbors: Neighbors of the polyhedron (the vertices).
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"""
Adds a polyhedron.
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train | StructureVis.add_triangle | Adds a triangular surface between three atoms.
Args:
atoms: Atoms between which a triangle will be drawn.
color: Color for triangle as RGB.
center: The "central atom" of the triangle
opacity: opacity of the triangle
draw_edges: If set to True, the a l... | pymatgen/vis/structure_vtk.py | def add_triangle(self, neighbors, color, center=None, opacity=0.4,
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edges_linewidth=2):
"""
Adds a triangular surface between three atoms.
Args:
atoms: Atoms between which a triangle will be draw... | def add_triangle(self, neighbors, color, center=None, opacity=0.4,
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edges_linewidth=2):
"""
Adds a triangular surface between three atoms.
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train | StructureVis.add_bonds | Adds bonds for a site.
Args:
neighbors: Neighbors of the site.
center: The site in the center for all bonds.
color: Color of the tubes representing the bonds
opacity: Opacity of the tubes representing the bonds
radius: Radius of tube s representing th... | pymatgen/vis/structure_vtk.py | def add_bonds(self, neighbors, center, color=None, opacity=None,
radius=0.1):
"""
Adds bonds for a site.
Args:
neighbors: Neighbors of the site.
center: The site in the center for all bonds.
color: Color of the tubes representing the bonds
... | def add_bonds(self, neighbors, center, color=None, opacity=None,
radius=0.1):
"""
Adds bonds for a site.
Args:
neighbors: Neighbors of the site.
center: The site in the center for all bonds.
color: Color of the tubes representing the bonds
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train | get_mi_vec | Convenience function which returns the unit vector aligned
with the miller index. | pymatgen/analysis/adsorption.py | def get_mi_vec(slab):
"""
Convenience function which returns the unit vector aligned
with the miller index.
"""
mvec = np.cross(slab.lattice.matrix[0], slab.lattice.matrix[1])
return mvec / np.linalg.norm(mvec) | def get_mi_vec(slab):
"""
Convenience function which returns the unit vector aligned
with the miller index.
"""
mvec = np.cross(slab.lattice.matrix[0], slab.lattice.matrix[1])
return mvec / np.linalg.norm(mvec) | [
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train | get_rot | Gets the transformation to rotate the z axis into the miller index | pymatgen/analysis/adsorption.py | def get_rot(slab):
"""
Gets the transformation to rotate the z axis into the miller index
"""
new_z = get_mi_vec(slab)
a, b, c = slab.lattice.matrix
new_x = a / np.linalg.norm(a)
new_y = np.cross(new_z, new_x)
x, y, z = np.eye(3)
rot_matrix = np.array([np.dot(*el) for el in
... | def get_rot(slab):
"""
Gets the transformation to rotate the z axis into the miller index
"""
new_z = get_mi_vec(slab)
a, b, c = slab.lattice.matrix
new_x = a / np.linalg.norm(a)
new_y = np.cross(new_z, new_x)
x, y, z = np.eye(3)
rot_matrix = np.array([np.dot(*el) for el in
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train | put_coord_inside | converts a cartesian coordinate such that it is inside the unit cell. | pymatgen/analysis/adsorption.py | def put_coord_inside(lattice, cart_coordinate):
"""
converts a cartesian coordinate such that it is inside the unit cell.
"""
fc = lattice.get_fractional_coords(cart_coordinate)
return lattice.get_cartesian_coords([c - np.floor(c) for c in fc]) | def put_coord_inside(lattice, cart_coordinate):
"""
converts a cartesian coordinate such that it is inside the unit cell.
"""
fc = lattice.get_fractional_coords(cart_coordinate)
return lattice.get_cartesian_coords([c - np.floor(c) for c in fc]) | [
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train | reorient_z | reorients a structure such that the z axis is concurrent with the
normal to the A-B plane | pymatgen/analysis/adsorption.py | def reorient_z(structure):
"""
reorients a structure such that the z axis is concurrent with the
normal to the A-B plane
"""
struct = structure.copy()
sop = get_rot(struct)
struct.apply_operation(sop)
return struct | def reorient_z(structure):
"""
reorients a structure such that the z axis is concurrent with the
normal to the A-B plane
"""
struct = structure.copy()
sop = get_rot(struct)
struct.apply_operation(sop)
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train | plot_slab | Function that helps visualize the slab in a 2-D plot, for
convenient viewing of output of AdsorbateSiteFinder.
Args:
slab (slab): Slab object to be visualized
ax (axes): matplotlib axes with which to visualize
scale (float): radius scaling for sites
repeat (int): number of repea... | pymatgen/analysis/adsorption.py | def plot_slab(slab, ax, scale=0.8, repeat=5, window=1.5,
draw_unit_cell=True, decay=0.2, adsorption_sites=True):
"""
Function that helps visualize the slab in a 2-D plot, for
convenient viewing of output of AdsorbateSiteFinder.
Args:
slab (slab): Slab object to be visualized
... | def plot_slab(slab, ax, scale=0.8, repeat=5, window=1.5,
draw_unit_cell=True, decay=0.2, adsorption_sites=True):
"""
Function that helps visualize the slab in a 2-D plot, for
convenient viewing of output of AdsorbateSiteFinder.
Args:
slab (slab): Slab object to be visualized
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train | AdsorbateSiteFinder.from_bulk_and_miller | This method constructs the adsorbate site finder from a bulk
structure and a miller index, which allows the surface sites
to be determined from the difference in bulk and slab coordination,
as opposed to the height threshold.
Args:
structure (Structure): structure from which... | pymatgen/analysis/adsorption.py | def from_bulk_and_miller(cls, structure, miller_index, min_slab_size=8.0,
min_vacuum_size=10.0, max_normal_search=None,
center_slab=True, selective_dynamics=False,
undercoord_threshold=0.09):
"""
This method construct... | def from_bulk_and_miller(cls, structure, miller_index, min_slab_size=8.0,
min_vacuum_size=10.0, max_normal_search=None,
center_slab=True, selective_dynamics=False,
undercoord_threshold=0.09):
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train | AdsorbateSiteFinder.find_surface_sites_by_height | This method finds surface sites by determining which sites are within
a threshold value in height from the topmost site in a list of sites
Args:
site_list (list): list of sites from which to select surface sites
height (float): threshold in angstroms of distance from topmost
... | pymatgen/analysis/adsorption.py | def find_surface_sites_by_height(self, slab, height=0.9, xy_tol=0.05):
"""
This method finds surface sites by determining which sites are within
a threshold value in height from the topmost site in a list of sites
Args:
site_list (list): list of sites from which to select su... | def find_surface_sites_by_height(self, slab, height=0.9, xy_tol=0.05):
"""
This method finds surface sites by determining which sites are within
a threshold value in height from the topmost site in a list of sites
Args:
site_list (list): list of sites from which to select su... | [
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train | AdsorbateSiteFinder.assign_site_properties | Assigns site properties. | pymatgen/analysis/adsorption.py | def assign_site_properties(self, slab, height=0.9):
"""
Assigns site properties.
"""
if 'surface_properties' in slab.site_properties.keys():
return slab
else:
surf_sites = self.find_surface_sites_by_height(slab, height)
surf_props = ['surface' if s... | def assign_site_properties(self, slab, height=0.9):
"""
Assigns site properties.
"""
if 'surface_properties' in slab.site_properties.keys():
return slab
else:
surf_sites = self.find_surface_sites_by_height(slab, height)
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train | AdsorbateSiteFinder.get_extended_surface_mesh | Gets an extended surface mesh for to use for adsorption
site finding by constructing supercell of surface sites
Args:
repeat (3-tuple): repeat for getting extended surface mesh | pymatgen/analysis/adsorption.py | def get_extended_surface_mesh(self, repeat=(5, 5, 1)):
"""
Gets an extended surface mesh for to use for adsorption
site finding by constructing supercell of surface sites
Args:
repeat (3-tuple): repeat for getting extended surface mesh
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Gets an extended surface mesh for to use for adsorption
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repeat (3-tuple): repeat for getting extended surface mesh
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train | AdsorbateSiteFinder.find_adsorption_sites | Finds surface sites according to the above algorithm. Returns
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Args:
distance (float): distance from the coordinating ensemble
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the distance from the slab itself... | pymatgen/analysis/adsorption.py | def find_adsorption_sites(self, distance=2.0, put_inside=True,
symm_reduce=1e-2, near_reduce=1e-2,
positions=['ontop', 'bridge', 'hollow'],
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train | AdsorbateSiteFinder.symm_reduce | Reduces the set of adsorbate sites by finding removing
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Args:
coords_set: coordinate set in cartesian coordinates
threshold: tolerance for distance equivalence, used
as input to in_coord_list_pbc for dupl. checking | pymatgen/analysis/adsorption.py | def symm_reduce(self, coords_set, threshold=1e-6):
"""
Reduces the set of adsorbate sites by finding removing
symmetrically equivalent duplicates
Args:
coords_set: coordinate set in cartesian coordinates
threshold: tolerance for distance equivalence, used
... | def symm_reduce(self, coords_set, threshold=1e-6):
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Reduces the set of adsorbate sites by finding removing
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coords_set: coordinate set in cartesian coordinates
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train | AdsorbateSiteFinder.near_reduce | Prunes coordinate set for coordinates that are within
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Args:
coords_set (Nx3 array-like): list or array of coordinates
threshold (float): threshold value for distance | pymatgen/analysis/adsorption.py | def near_reduce(self, coords_set, threshold=1e-4):
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Prunes coordinate set for coordinates that are within
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Args:
coords_set (Nx3 array-like): list or array of coordinates
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Prunes coordinate set for coordinates that are within
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coords_set (Nx3 array-like): list or array of coordinates
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train | AdsorbateSiteFinder.ensemble_center | Finds the center of an ensemble of sites selected from
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algorithm.
Args:
site_list (list of sites): list of sites
indices (list of ints): list of ints from which to select
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... | pymatgen/analysis/adsorption.py | def ensemble_center(self, site_list, indices, cartesian=True):
"""
Finds the center of an ensemble of sites selected from
a list of sites. Helper method for the find_adsorption_sites
algorithm.
Args:
site_list (list of sites): list of sites
indices (list... | def ensemble_center(self, site_list, indices, cartesian=True):
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Finds the center of an ensemble of sites selected from
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site_list (list of sites): list of sites
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train | AdsorbateSiteFinder.add_adsorbate | Adds an adsorbate at a particular coordinate. Adsorbate
represented by a Molecule object, and is positioned relative
to the input adsorbate coordinate.
Args:
molecule (Molecule): molecule object representing the adsorbate
ads_coord (array): coordinate of adsorbate posit... | pymatgen/analysis/adsorption.py | def add_adsorbate(self, molecule, ads_coord, repeat=None, reorient=True):
"""
Adds an adsorbate at a particular coordinate. Adsorbate
represented by a Molecule object, and is positioned relative
to the input adsorbate coordinate.
Args:
molecule (Molecule): molecule ... | def add_adsorbate(self, molecule, ads_coord, repeat=None, reorient=True):
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Adds an adsorbate at a particular coordinate. Adsorbate
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train | AdsorbateSiteFinder.assign_selective_dynamics | Helper function to assign selective dynamics site_properties
based on surface, subsurface site properties
Args:
slab (Slab): slab for which to assign selective dynamics | pymatgen/analysis/adsorption.py | def assign_selective_dynamics(self, slab):
"""
Helper function to assign selective dynamics site_properties
based on surface, subsurface site properties
Args:
slab (Slab): slab for which to assign selective dynamics
"""
sd_list = []
sd_list = [[False,... | def assign_selective_dynamics(self, slab):
"""
Helper function to assign selective dynamics site_properties
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Args:
slab (Slab): slab for which to assign selective dynamics
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sd_list = []
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train | AdsorbateSiteFinder.generate_adsorption_structures | Function that generates all adsorption structures for a given
molecular adsorbate. Can take repeat argument or minimum
length/width of precursor slab as an input
Args:
molecule (Molecule): molecule corresponding to adsorbate
repeat (3-tuple or list): repeat argument for... | pymatgen/analysis/adsorption.py | def generate_adsorption_structures(self, molecule, repeat=None, min_lw=5.0,
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"""
Function that generates all adsorption structures for a given
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length/width of pre... | def generate_adsorption_structures(self, molecule, repeat=None, min_lw=5.0,
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train | AdsorbateSiteFinder.adsorb_both_surfaces | Function that generates all adsorption structures for a given
molecular adsorbate on both surfaces of a slab. This is useful
for calculating surface energy where both surfaces need to be
equivalent or if we want to calculate nonpolar systems.
Args:
molecule (Molecule): molec... | pymatgen/analysis/adsorption.py | def adsorb_both_surfaces(self, molecule, repeat=None, min_lw=5.0,
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"""
Function that generates all adsorption structures for a given
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train | AdsorbateSiteFinder.generate_substitution_structures | Function that performs substitution-type doping on the surface and
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per surface. Can substitute one surface or both.
Args:
atom (str): atom corresponding to substitutional dopant
sub_both_sides (b... | pymatgen/analysis/adsorption.py | def generate_substitution_structures(self, atom, target_species=[],
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dist_from_surf=0):
"""
Function that performs substitution-type doping on the surface and
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train | ExcitingInput.from_string | Reads the exciting input from a string | pymatgen/io/exciting/inputs.py | def from_string(data):
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Reads the exciting input from a string
"""
root=ET.fromstring(data)
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title_in=str(ro... | def from_string(data):
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train | SiteCollection.types_of_specie | List of types of specie. Only works for ordered structures.
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"""
List of types of specie. Only works for ordered structures.
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"""
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raise TypeError("""\
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... | def types_of_specie(self):
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List of types of specie. Only works for ordered structures.
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train | SiteCollection.group_by_types | Iterate over species grouped by type | pymatgen/core/structure.py | def group_by_types(self):
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for t in self.types_of_specie:
for site in self:
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train | SiteCollection.indices_from_symbol | Returns a tuple with the sequential indices of the sites
that contain an element with the given chemical symbol. | pymatgen/core/structure.py | def indices_from_symbol(self, symbol: str) -> tuple:
"""
Returns a tuple with the sequential indices of the sites
that contain an element with the given chemical symbol.
"""
return tuple((i for i, specie in enumerate(self.species)
if specie.symbol == symbol)... | def indices_from_symbol(self, symbol: str) -> tuple:
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train | SiteCollection.site_properties | Returns the site properties as a dict of sequences. E.g.,
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"""
Returns the site properties as a dict of sequences. E.g.,
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"""
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prop_keys = set()
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Returns the site properties as a dict of sequences. E.g.,
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train | SiteCollection.composition | (Composition) Returns the composition | pymatgen/core/structure.py | def composition(self):
"""
(Composition) Returns the composition
"""
elmap = collections.defaultdict(float)
for site in self:
for species, occu in site.species.items():
elmap[species] += occu
return Composition(elmap) | def composition(self):
"""
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elmap = collections.defaultdict(float)
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elmap[species] += occu
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train | SiteCollection.charge | Returns the net charge of the structure based on oxidation states. If
Elements are found, a charge of 0 is assumed. | pymatgen/core/structure.py | def charge(self):
"""
Returns the net charge of the structure based on oxidation states. If
Elements are found, a charge of 0 is assumed.
"""
charge = 0
for site in self:
for specie, amt in site.species.items():
charge += getattr(specie, "oxi_s... | def charge(self):
"""
Returns the net charge of the structure based on oxidation states. If
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"""
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train | SiteCollection.get_angle | Returns angle specified by three sites.
Args:
i: Index of first site.
j: Index of second site.
k: Index of third site.
Returns:
Angle in degrees. | pymatgen/core/structure.py | def get_angle(self, i: int, j: int, k: int) -> float:
"""
Returns angle specified by three sites.
Args:
i: Index of first site.
j: Index of second site.
k: Index of third site.
Returns:
Angle in degrees.
"""
v1 = self[i].c... | def get_angle(self, i: int, j: int, k: int) -> float:
"""
Returns angle specified by three sites.
Args:
i: Index of first site.
j: Index of second site.
k: Index of third site.
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"""
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train | SiteCollection.get_dihedral | Returns dihedral angle specified by four sites.
Args:
i: Index of first site
j: Index of second site
k: Index of third site
l: Index of fourth site
Returns:
Dihedral angle in degrees. | pymatgen/core/structure.py | def get_dihedral(self, i: int, j: int, k: int, l: int) -> float:
"""
Returns dihedral angle specified by four sites.
Args:
i: Index of first site
j: Index of second site
k: Index of third site
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Returns:
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"""
Returns dihedral angle specified by four sites.
Args:
i: Index of first site
j: Index of second site
k: Index of third site
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train | SiteCollection.is_valid | True if SiteCollection does not contain atoms that are too close
together. Note that the distance definition is based on type of
SiteCollection. Cartesian distances are used for non-periodic
Molecules, while PBC is taken into account for periodic structures.
Args:
tol (float... | pymatgen/core/structure.py | def is_valid(self, tol: float = DISTANCE_TOLERANCE) -> bool:
"""
True if SiteCollection does not contain atoms that are too close
together. Note that the distance definition is based on type of
SiteCollection. Cartesian distances are used for non-periodic
Molecules, while PBC is ... | def is_valid(self, tol: float = DISTANCE_TOLERANCE) -> bool:
"""
True if SiteCollection does not contain atoms that are too close
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train | SiteCollection.add_site_property | Adds a property to a site.
Args:
property_name (str): The name of the property to add.
values (list): A sequence of values. Must be same length as
number of sites. | pymatgen/core/structure.py | def add_site_property(self, property_name, values):
"""
Adds a property to a site.
Args:
property_name (str): The name of the property to add.
values (list): A sequence of values. Must be same length as
number of sites.
"""
if len(values) ... | def add_site_property(self, property_name, values):
"""
Adds a property to a site.
Args:
property_name (str): The name of the property to add.
values (list): A sequence of values. Must be same length as
number of sites.
"""
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train | SiteCollection.replace_species | Swap species.
Args:
species_mapping (dict): dict of species to swap. Species can be
elements too. E.g., {Element("Li"): Element("Na")} performs
a Li for Na substitution. The second species can be a
sp_and_occu dict. For example, a site with 0.5 Si tha... | pymatgen/core/structure.py | def replace_species(self, species_mapping):
"""
Swap species.
Args:
species_mapping (dict): dict of species to swap. Species can be
elements too. E.g., {Element("Li"): Element("Na")} performs
a Li for Na substitution. The second species can be a
... | def replace_species(self, species_mapping):
"""
Swap species.
Args:
species_mapping (dict): dict of species to swap. Species can be
elements too. E.g., {Element("Li"): Element("Na")} performs
a Li for Na substitution. The second species can be a
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train | SiteCollection.add_oxidation_state_by_element | Add oxidation states.
Args:
oxidation_states (dict): Dict of oxidation states.
E.g., {"Li":1, "Fe":2, "P":5, "O":-2} | pymatgen/core/structure.py | def add_oxidation_state_by_element(self, oxidation_states):
"""
Add oxidation states.
Args:
oxidation_states (dict): Dict of oxidation states.
E.g., {"Li":1, "Fe":2, "P":5, "O":-2}
"""
try:
for site in self.sites:
new_sp = ... | def add_oxidation_state_by_element(self, oxidation_states):
"""
Add oxidation states.
Args:
oxidation_states (dict): Dict of oxidation states.
E.g., {"Li":1, "Fe":2, "P":5, "O":-2}
"""
try:
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train | SiteCollection.add_oxidation_state_by_site | Add oxidation states to a structure by site.
Args:
oxidation_states (list): List of oxidation states.
E.g., [1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 5, -2, -2, -2, -2] | pymatgen/core/structure.py | def add_oxidation_state_by_site(self, oxidation_states):
"""
Add oxidation states to a structure by site.
Args:
oxidation_states (list): List of oxidation states.
E.g., [1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 5, -2, -2, -2, -2]
"""
if len(oxidation_states) ... | def add_oxidation_state_by_site(self, oxidation_states):
"""
Add oxidation states to a structure by site.
Args:
oxidation_states (list): List of oxidation states.
E.g., [1, 1, 1, 1, 2, 2, 2, 2, 5, 5, 5, 5, -2, -2, -2, -2]
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train | SiteCollection.remove_oxidation_states | Removes oxidation states from a structure. | pymatgen/core/structure.py | def remove_oxidation_states(self):
"""
Removes oxidation states from a structure.
"""
for site in self.sites:
new_sp = collections.defaultdict(float)
for el, occu in site.species.items():
sym = el.symbol
new_sp[Element(sym)] += occu... | def remove_oxidation_states(self):
"""
Removes oxidation states from a structure.
"""
for site in self.sites:
new_sp = collections.defaultdict(float)
for el, occu in site.species.items():
sym = el.symbol
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train | SiteCollection.add_oxidation_state_by_guess | Decorates the structure with oxidation state, guessing
using Composition.oxi_state_guesses()
Args:
**kwargs: parameters to pass into oxi_state_guesses() | pymatgen/core/structure.py | def add_oxidation_state_by_guess(self, **kwargs):
"""
Decorates the structure with oxidation state, guessing
using Composition.oxi_state_guesses()
Args:
**kwargs: parameters to pass into oxi_state_guesses()
"""
oxid_guess = self.composition.oxi_state_guesses(... | def add_oxidation_state_by_guess(self, **kwargs):
"""
Decorates the structure with oxidation state, guessing
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Args:
**kwargs: parameters to pass into oxi_state_guesses()
"""
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train | SiteCollection.add_spin_by_element | Add spin states to a structure.
Args:
spisn (dict): Dict of spins associated with
elements or species, e.g. {"Ni":+5} or {"Ni2+":5} | pymatgen/core/structure.py | def add_spin_by_element(self, spins):
"""
Add spin states to a structure.
Args:
spisn (dict): Dict of spins associated with
elements or species, e.g. {"Ni":+5} or {"Ni2+":5}
"""
for site in self.sites:
new_sp = {}
for sp, occu in s... | def add_spin_by_element(self, spins):
"""
Add spin states to a structure.
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spisn (dict): Dict of spins associated with
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train | SiteCollection.add_spin_by_site | Add spin states to a structure by site.
Args:
spins (list): List of spins
E.g., [+5, -5, 0, 0] | pymatgen/core/structure.py | def add_spin_by_site(self, spins):
"""
Add spin states to a structure by site.
Args:
spins (list): List of spins
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if len(spins) != len(self.sites):
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Add spin states to a structure by site.
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spins (list): List of spins
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] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L463-L482 | [
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train | SiteCollection.remove_spin | Removes spin states from a structure. | pymatgen/core/structure.py | def remove_spin(self):
"""
Removes spin states from a structure.
"""
for site in self.sites:
new_sp = collections.defaultdict(float)
for sp, occu in site.species.items():
oxi_state = getattr(sp, "oxi_state", None)
new_sp[Specie(sp.s... | def remove_spin(self):
"""
Removes spin states from a structure.
"""
for site in self.sites:
new_sp = collections.defaultdict(float)
for sp, occu in site.species.items():
oxi_state = getattr(sp, "oxi_state", None)
new_sp[Specie(sp.s... | [
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] | materialsproject/pymatgen | python | https://github.com/materialsproject/pymatgen/blob/4ca558cf72f8d5f8a1f21dfdfc0181a971c186da/pymatgen/core/structure.py#L484-L493 | [
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"... | 4ca558cf72f8d5f8a1f21dfdfc0181a971c186da |
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